I go the answer from another user here at Panasonic.
Hi Im new to pads and im facing the same problem.
Can you give the solution for this.
Thanks in Advance.
By now you probably found an answer.
Just in case here is what the solution was for Expedition;
The symbol that locates the drill symbols has an origin, I overlaid that origin with the Gerber origin and the drill symbols lined up.
Perhaps you have the same misalignment.
I hope this helps.
Try regenerating the NC drill file after rotating the design (Output>NC Drill... from the Expedition menu).